Genotyping and Sequencing Technologies in Population Genetics and Genomics

2018 ◽  
pp. 83-125 ◽  
Author(s):  
J. A. Holliday ◽  
E. M. Hallerman ◽  
D. C. Haak
Keyword(s):  
Population Genetics ◽  
Sequencing Technologies ◽  
Genetics And Genomics

A Primer of Population Genetics and Genomics

2020 ◽  
Author(s):  
Daniel L. Hartl
Keyword(s):  
Population Genetics ◽  
Complex Traits ◽  
Evolutionary Biology ◽  
Knowledge Retention ◽  
Learning By Doing ◽  
Human Populations ◽  
Gene Drive ◽  
Molecular Population Genetics ◽  
Genetics And Genomics ◽  
And Mathematics

A Primer of Population Genetics and Genomics, 4th edition, has been completely revised and updated to provide a concise but comprehensive introduction to the basic concepts of population genetics and genomics. Recent textbooks have tended to focus on such specialized topics as the coalescent, molecular evolution, human population genetics, or genomics. This primer bucks that trend by encouraging a broader familiarity with, and understanding of, population genetics and genomics as a whole. The overview ranges from mating systems through the causes of evolution, molecular population genetics, and the genomics of complex traits. Interwoven are discussions of ancient DNA, gene drive, landscape genetics, identifying risk factors for complex diseases, the genomics of adaptation and speciation, and other active areas of research. The principles are illuminated by numerous examples from a wide variety of animals, plants, microbes, and human populations. The approach also emphasizes learning by doing, which in this case means solving numerical or conceptual problems. The rationale behind this is that the use of concepts in problem-solving lead to deeper understanding and longer knowledge retention. This accessible, introductory textbook is aimed principally at students of various levels and abilities (from senior undergraduate to postgraduate) as well as practising scientists in the fields of population genetics, ecology, evolutionary biology, computational biology, bioinformatics, biostatistics, physics, and mathematics.

scholarly journals Population Genomic- and Phylogenomic-Enabled Advances to Increase Insight Into Pathogen Biology and Epidemiology

2021 ◽  
Vol 111 (1) ◽  
pp. 8-11
Author(s):  
Remco Stam ◽  
Pierre Gladieux ◽  
Boris A. Vinatzer ◽  
Erica M. Goss ◽  
Neha Potnis ◽  
...  
Keyword(s):  
Population Genetics ◽  
Population Genomics ◽  
Cost Effective ◽  
Whole Genome ◽  
Genome Data ◽  
Sequencing Technologies ◽  
Population Genomic ◽  
High Throughput Dna Sequencing ◽  
Opening Up ◽  
Insight Into

Population genetics has been a key discipline in phytopathology for many years. The recent rise in cost-effective, high-throughput DNA sequencing technologies, allows sequencing of dozens, if not hundreds of specimens, turning population genetics into population genomics and opening up new, exciting opportunities as described in this Focus Issue . Without the limitations of genetic markers and the availability of whole or near whole-genome data, population genomics can give new insights into the biology, evolution and adaptation, and dissemination patterns of plant-associated microbes.

scholarly journals Union of phylogeography and landscape genetics

2016 ◽  
Vol 113 (29) ◽  
pp. 8079-8086 ◽  
Author(s):  
Leslie J. Rissler
Keyword(s):  
Population Genetics ◽  
Landscape Genetics ◽  
Mojave Desert ◽  
Spatially Explicit ◽  
Novel Studies ◽  
Biology I ◽  
Genomic Scale ◽  
Genetics And Genomics ◽  
Lineage Divergence ◽  
Scale Data

Phylogeography and landscape genetics have arisen within the past 30 y. Phylogeography is said to be the bridge between population genetics and systematics, and landscape genetics the bridge between landscape ecology and population genetics. Both fields can be considered as simply the amalgamation of classic biogeography with genetics and genomics; however, they differ in the temporal, spatial, and organismal scales addressed and the methodology used. I begin by briefly summarizing the history and purview of each field and suggest that, even though landscape genetics is a younger field (coined in 2003) than phylogeography (coined in 1987), early studies by Dobzhansky on the “microgeographic races” of Linanthus parryae in the Mojave Desert of California and Drosophila pseudoobscura across the western United States presaged the fields by over 40 y. Recent advances in theory, models, and methods have allowed researchers to better synthesize ecological and evolutionary processes in their quest to answer some of the most basic questions in biology. I highlight a few of these novel studies and emphasize three major areas ripe for investigation using spatially explicit genomic-scale data: the biogeography of speciation, lineage divergence and species delimitation, and understanding adaptation through time and space. Examples of areas in need of study are highlighted, and I end by advocating a union of phylogeography and landscape genetics under the more general field: biogeography.

scholarly journals Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud)

Plants ◽  
2019 ◽  
Vol 8 (10) ◽  
pp. 376
Author(s):  
Peterson W. Wambugu ◽  
Marie-Noelle Ndjiondjop ◽  
Robert Henry
Keyword(s):  
Oryza Glaberrima ◽  
Trait Variation ◽  
African Rice ◽  
Sequencing Technologies ◽  
Climate Resilience ◽  
Sequencing Studies ◽  
Important Trait ◽  
Genetics And Genomics ◽  
Rice Improvement ◽  
Rice Genetic

African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.

scholarly journals Chromoblastomycosis Caused by Phialophora—Proven Cases from Mexico

2021 ◽  
Vol 7 (2) ◽  
pp. 95
Author(s):  
Sarah A. Ahmed ◽  
Alexandro Bonifaz ◽  
Gloria M. González ◽  
Leandro F. Moreno ◽  
Nickolas Menezes da Silva ◽  
...  
Keyword(s):  
Population Genetics ◽  
Clinical Strains ◽  
Phialophora Verrucosa ◽  
Etiologic Agents ◽  
Genetics And Genomics

Chromoblastomycosis is a chronic severely mutilating disease caused by fungi of the order Chaetothyriales. Classically, Phialophora verrucosa has been listed among these etiologic agents. This species is known to occur in the environment and has been found to cause other infections like phaeohyphomycosis, while reported cases of chromoblastomycosis are scant. Phialophora is phylogenetically diverse, and thus retrospective confirmation of etiology is necessary. We studied ten proven cases of chromoblastomycosis from Mexico and further analyzed the population genetics and genomics of the Phialophora species to understand their pathogenicity and predilection. The clinical strains were molecularly identified as Phialophora americana (n = 4), Phialophorachinensis (n = 4), and Phialophora macrospora (n = 2). No genetic distinction between clinical and environmental strains was possible. Further analysis of strains from diverse origins are needed to address eventual differences in virulence and niche predilection between the species.

scholarly journals Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations

2022 ◽  
Author(s):  
Claire E Couch ◽  
Clinton W Epps
Keyword(s):  
Population Genetics ◽  
Gut Microbiome ◽  
Landscape Heterogeneity ◽  
Natural Populations ◽  
Host Population ◽  
Model Organisms ◽  
Wild Populations ◽  
Sequencing Technologies ◽  
Wild Host ◽  
Wide Range

Abstract In recent years, emerging sequencing technologies and computational tools have driven a tidal wave of research on host-associated microbiomes, particularly the gut microbiome. These studies demonstrate numerous connections between the gut microbiome and vital host functions, primarily in humans, model organisms, and domestic animals. As the adaptive importance of the gut microbiome becomes clearer, interest in studying the gut microbiomes of wild populations has increased, in part due to the potential for discovering conservation applications. The study of wildlife gut microbiomes holds many new challenges and opportunities due to the complex genetic, spatial, and environmental structure of wild host populations, and the potential for these factors to interact with the microbiome. The emerging picture of adaptive coevolution in host-microbiome relationships highlights the importance of understanding microbiome variation in the context of host population genetics and landscape heterogeneity across a wide range of host populations. We propose a conceptual framework for understanding wildlife gut microbiomes in relation to landscape variables and host population genetics, including the potential of approaches derived from landscape genetics. We use this framework to review current research, synthesize important trends, highlight implications for conservation, and recommend future directions for research. Specifically, we focus on how spatial structure and environmental variation interact with host population genetics and microbiome variation in natural populations, and what we can learn from how these patterns of covariation differ depending on host ecological and evolutionary traits.

Abstracts of the International Workshop “ONYGENALES 2020: Basic and Clinical Research Advances in Dermatophytes and Dimorphic Fungi”.

2020 ◽  
Vol 72 (2) ◽  
pp. 163-198
Keyword(s):  
Public Health ◽  
Population Genetics ◽  
Health Professionals ◽  
Susceptibility Testing ◽  
International Workshop ◽  
Keratinophilic Fungi ◽  
Testing Session ◽  
Dimorphic Fungi ◽  
Public Health Professionals ◽  
Genetics And Genomics

The ONYGENALES workshop is a bi-annual meeting organised by ISHAM Working Group ONYGENALES (onygenales.org). It brings together researchers, students, clinicians, laboratorians and public health professionals across biomedical disciplines, who are interested in current developments in dermatophyte, dimorphic and keratinophilic fungi research. The abstracts are arranged according to the thematic sessions as they appeared in the programme: Session 1: Antifungal resistance and susceptibility testing, Session 2: Taxonomy of keratinophilic and dimorphic fungi, Session 3: Taxonomy of dermatophytes, Session 4: Population genetics and genomics, Session 5: Emerging and zoonotic pathogens, Session 6: Epidemiology, Session 7: Diagnostics and treatment approaches, Session 8: Virulence factors and pathogenesis.

Identification and Clinical Implications of a Novel MYO15A Variant in a Consanguineous Iranian Family by Targeted Exome Sequencing

2019 ◽  
Vol 24 (1) ◽  
pp. 25-31 ◽  
Author(s):  
Narges Zarepour ◽  
Mahbobeh Koohiyan ◽  
Afsaneh Taghipour-Sheshdeh ◽  
Fatemeh Nemati-Zargaran ◽  
Nader Saki ◽  
...  
Keyword(s):  
Pedigree Analysis ◽  
Genetic Linkage Analysis ◽  
Clinical Evaluations ◽  
Sequencing Technologies ◽  
The Family ◽  
New Strategy ◽  
Genetics And Genomics ◽  
Next Generation Sequencing Ngs ◽  
Very High ◽  
Generation Sequencing

Background and Objectives: Hereditary hearing loss (HL) is known by a very high genetic heterogeneity, which makes a molecular diagnosis problematic. Next-generation sequencing (NGS) is a new strategy that can overcome this problem. Method: A comprehensive family history was obtained, and clinical evaluations and pedigree analysis were performed in the family with 3 affected members. After excluding mutations in the GJB2 and 7 other most common autosomal recessive nonsyndromic HL genes via Sanger sequencing and genetic linkage analysis in the family, we applied the Otogenetics deafness NGS panel in the proband of this family. Results: NGS results showed a novel rare variant (c.7720C>T) in the MYO15A gene. This nonsense variant in the exon 40 of the MYO15A gene fulfills the criteria of being categorized as pathogenic according to the American College of Medical Genetics and Genomics guideline. Conclusions: New DNA sequencing technologies could lead to identification of the disease causing variants in highly heterogeneous disorders such as HL.

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